I don't disagree, I understand completely why it was done. With neither of our best holding midfielders up to full fitness, he didn't have a reliable option to play in the midfield other than Lahm (or Kramer...), and it was really our best option to work like that there. Also, we weren't sure if Klose could really perform anymore, so trying out the pivoting top three was fine, if unsuccessful due to poor performances from Götze in particular (poor guy, not being used right). Mustafi being out really gave Lahm the ability to prove how much more vital he was as a fullback, and the midfield looked a lot stronger with Khedira and Lahm not competing for attacking space on the right from the middle. This allowed Khedira to have much more control of his spot, Kroos to play centrally as he should, and Schweinsteiger to pull up and hold on the left. Also, being able to add Klose in actually helped a ton, as Müller was able to swing in from the right and float more than before, since he had to occupy a more central area to make up for the lack of striker. Now we can manage having a true finisher as well as the floating mastermind of Müller with no trouble. If Reus were around, no matter how clinical and amazing he is, I don't know if he would entirely improve this side without taking out Özil. Assuming that were the case though, we'd have the best front three in the tournament I think, if we don't already. Reus also makes up for defense issues, unlike Özil (as good as both are).
Honestly though, as much credit as we are giving Löw, I think some of this success was partly by accident. Mustafi getting hurt was really what caused all these things to be shown to him, even if everyone else in the world already knew it. Can't not add that last bit. Either way, when Klose is unable to play, I imagine a 4-3-3 would be extremely solid, with I guess Özil being safe in the middle spot, seeing as both Reus and Müller would be making cutting runs to make up for one person being gone. This would also allow for Lahm to play as a good attacking fullback, if he ages well, and Özil to make his best creative work possible. Kroos would still be fine, Schweinsteiger, Khedira, Hummels, all fine. Though I think I would rather have Badstuber than Boateng, and we desperately need a better LB.